ProteinDumper

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ProteinDumper

Scooter Willis-2

I added in ProteinDumper plugin and when selected I get a new browser window with a selected gene but no protein sequence. Any suggestions on what would result in an empty page. In HTML mode I do get the scaffold/range with the following HTML. I have the glyph type as gene and wonder if a specific feature type is required for ProteinDumper to recognize the CDS/Exon region.

Thanks

Scooter

<!DOCTYPE html
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en-US" xml:lang="en-US">
<head>
<title>scaffold00071:2589833..2591388</title>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
</head>
<body>
<h1>scaffold00071:2589833..2591388</h1><pre></pre>
</body>
</html>


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Re: ProteinDumper

Scott Cain
Hi Scooter,

What GBrowse version are you using, what database adaptor, and do you get any useful information from the apache error_log?

When I tried this dumper with the Chado adaptor on GBrowse2, I got a helpful message in the error log (a malformed sql query--it must be doing something I didn't expect).  However, when I do this with the Bio::DB::SeqFeature::Store memory adaptor and GBrowse2, I got what it looks like you got and no error message (making life a little more difficult).  My guess is you're the first person to try this dumper in a while.

Scott


On Thu, Jul 8, 2010 at 8:42 AM, Scooter Willis <[hidden email]> wrote:

I added in ProteinDumper plugin and when selected I get a new browser window with a selected gene but no protein sequence. Any suggestions on what would result in an empty page. In HTML mode I do get the scaffold/range with the following HTML. I have the glyph type as gene and wonder if a specific feature type is required for ProteinDumper to recognize the CDS/Exon region.

Thanks

Scooter

<!DOCTYPE html
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en-US" xml:lang="en-US">
<head>
<title>scaffold00071:2589833..2591388</title>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
</head>
<body>
<h1>scaffold00071:2589833..2591388</h1><pre></pre>
</body>
</html>


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------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: ProteinDumper

Scooter Willis-2
Scott

Any thoughts on how to get the ProteinDumper plugin working again?

Thanks

Scooter

________________________________________
From: Scott Cain [[hidden email]]
Sent: Thursday, July 08, 2010 9:55 AM
To: Scooter Willis
Cc: [hidden email]
Subject: Re: [GMOD-devel] ProteinDumper

Hi Scooter,

What GBrowse version are you using, what database adaptor, and do you get any useful information from the apache error_log?

When I tried this dumper with the Chado adaptor on GBrowse2, I got a helpful message in the error log (a malformed sql query--it must be doing something I didn't expect).  However, when I do this with the Bio::DB::SeqFeature::Store memory adaptor and GBrowse2, I got what it looks like you got and no error message (making life a little more difficult).  My guess is you're the first person to try this dumper in a while.

Scott


On Thu, Jul 8, 2010 at 8:42 AM, Scooter Willis <[hidden email]<mailto:[hidden email]>> wrote:

I added in ProteinDumper plugin and when selected I get a new browser window with a selected gene but no protein sequence. Any suggestions on what would result in an empty page. In HTML mode I do get the scaffold/range with the following HTML. I have the glyph type as gene and wonder if a specific feature type is required for ProteinDumper to recognize the CDS/Exon region.

Thanks

Scooter

        <!DOCTYPE html
        PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
        "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
        <html xmlns="http://www.w3.org/1999/xhtml" lang="en-US" xml:lang="en-US">
        <head>
        <title>scaffold00071:2589833..2591388</title>
        <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
        </head>
        <body>
        <h1>scaffold00071:2589833..2591388</h1><pre></pre>
        </body>
        </html>


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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: ProteinDumper

Dave Clements, GMOD Help Desk-3
Hi Scooter,

There hasn't been serious work done on this plugin for almost 4 years.

Is there anyone out there who is knowledgeable about GBrowse plugins who can take a look at this?  The plugin is less than 300 lines of perl:


Thanks,

Dave C

On Thu, Jul 15, 2010 at 7:57 AM, Scooter Willis <[hidden email]> wrote:
Scott

Any thoughts on how to get the ProteinDumper plugin working again?

Thanks

Scooter

________________________________________
From: Scott Cain [[hidden email]]
Sent: Thursday, July 08, 2010 9:55 AM
To: Scooter Willis
Subject: Re: [GMOD-devel] ProteinDumper

Hi Scooter,

What GBrowse version are you using, what database adaptor, and do you get any useful information from the apache error_log?

When I tried this dumper with the Chado adaptor on GBrowse2, I got a helpful message in the error log (a malformed sql query--it must be doing something I didn't expect).  However, when I do this with the Bio::DB::SeqFeature::Store memory adaptor and GBrowse2, I got what it looks like you got and no error message (making life a little more difficult).  My guess is you're the first person to try this dumper in a while.

Scott


On Thu, Jul 8, 2010 at 8:42 AM, Scooter Willis <[hidden email]<mailto:[hidden email]>> wrote:

I added in ProteinDumper plugin and when selected I get a new browser window with a selected gene but no protein sequence. Any suggestions on what would result in an empty page. In HTML mode I do get the scaffold/range with the following HTML. I have the glyph type as gene and wonder if a specific feature type is required for ProteinDumper to recognize the CDS/Exon region.

Thanks

Scooter

       <!DOCTYPE html
       PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
       "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
       <html xmlns="http://www.w3.org/1999/xhtml" lang="en-US" xml:lang="en-US">
       <head>
       <title>scaffold00071:2589833..2591388</title>
       <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
       </head>
       <body>
       <h1>scaffold00071:2589833..2591388</h1><pre></pre>
       </body>
       </html>


------------------------------------------------------------------------------
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: ProteinDumper

Scooter Willis-2
Dave

I wanted to see if you had any response or discussions about getting ProteinDumper plugin fixed? I would imagine it should be fairly straight forward for an experienced GBrowse/Perl developer to figure out what has changed. From Scott's email below using Chado he gets a malformed sql query and in the memory adaptor just a blank page. 

Thanks

Scooter

On Jul 20, 2010, at 4:02 PM, Dave Clements, GMOD Help Desk wrote:

Hi Scooter,

There hasn't been serious work done on this plugin for almost 4 years.

Is there anyone out there who is knowledgeable about GBrowse plugins who can take a look at this?  The plugin is less than 300 lines of perl:


Thanks,

Dave C

On Thu, Jul 15, 2010 at 7:57 AM, Scooter Willis <[hidden email]> wrote:
Scott

Any thoughts on how to get the ProteinDumper plugin working again?

Thanks

Scooter

________________________________________
From: Scott Cain [[hidden email]]
Sent: Thursday, July 08, 2010 9:55 AM
To: Scooter Willis
Subject: Re: [GMOD-devel] ProteinDumper

Hi Scooter,

What GBrowse version are you using, what database adaptor, and do you get any useful information from the apache error_log?

When I tried this dumper with the Chado adaptor on GBrowse2, I got a helpful message in the error log (a malformed sql query--it must be doing something I didn't expect).  However, when I do this with the Bio::DB::SeqFeature::Store memory adaptor and GBrowse2, I got what it looks like you got and no error message (making life a little more difficult).  My guess is you're the first person to try this dumper in a while.

Scott


On Thu, Jul 8, 2010 at 8:42 AM, Scooter Willis <[hidden email]<mailto:[hidden email]>> wrote:

I added in ProteinDumper plugin and when selected I get a new browser window with a selected gene but no protein sequence. Any suggestions on what would result in an empty page. In HTML mode I do get the scaffold/range with the following HTML. I have the glyph type as gene and wonder if a specific feature type is required for ProteinDumper to recognize the CDS/Exon region.

Thanks

Scooter

       <!DOCTYPE html
       PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
       "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
       <html xmlns="http://www.w3.org/1999/xhtml" lang="en-US" xml:lang="en-US">
       <head>
       <title>scaffold00071:2589833..2591388</title>
       <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
       </head>
       <body>
       <h1>scaffold00071:2589833..2591388</h1><pre></pre>
       </body>
       </html>


------------------------------------------------------------------------------
This SF.net email is sponsored by Sprint
What will you do first with EVO, the first 4G phone?
Visit sprint.com/first<http://sprint.com/first> -- http://p.sf.net/sfu/sprint-com-first
_______________________________________________
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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--
===> PLEASE KEEP RESPONSES ON THE LIST <===
http://gmod.org/wiki/GMOD_News
http://gmod.org/wiki/Calendar
http://gmod.org/wiki/Help_Desk_Feedback



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